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RIP-chip-SRM--a new combinatorial large-scale approach identifies a set of translationally regulated bantam/miR-58 targets in C. elegans.

Jovanovic, M, Reiter, L, Clark, A, Weiss, M, Picotti, P, Rehrauer, H, Frei, A, Neukomm, LJ, Kaufman, E, Wollscheid, B, Simard, MJ, Miska, EA, Aebersold, R, Gerber, AP and Hengartner, MO (2012) RIP-chip-SRM--a new combinatorial large-scale approach identifies a set of translationally regulated bantam/miR-58 targets in C. elegans. Genome Res.

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Abstract

MicroRNAs (miRNAs) are small, noncoding RNAs that negatively regulate gene expression. As miRNAs are involved in a wide range of biological processes and diseases, much effort has been invested in identifying their mRNA targets. Here, we present a novel combinatorial approach, RIP-chip-SRM (RNA-binding protein immunopurification + microarray + targeted protein quantification via selected reaction monitoring), to identify de novo high-confidence miRNA targets in the nematode Caenorhabditis elegans. We used differential RIP-chip analysis of miRNA-induced silencing complexes from wild-type and miRNA mutant animals, followed by quantitative targeted proteomics via selected reaction monitoring to identify and validate mRNA targets of the C. elegans bantam homolog miR-58. Comparison of total mRNA and protein abundance changes in mir-58 mutant and wild-type animals indicated that the direct bantam/miR-58 targets identified here are mainly regulated at the level of protein abundance, not mRNA stability.

Item Type: Article
Authors :
AuthorsEmailORCID
Jovanovic, MUNSPECIFIEDUNSPECIFIED
Reiter, LUNSPECIFIEDUNSPECIFIED
Clark, AUNSPECIFIEDUNSPECIFIED
Weiss, MUNSPECIFIEDUNSPECIFIED
Picotti, PUNSPECIFIEDUNSPECIFIED
Rehrauer, HUNSPECIFIEDUNSPECIFIED
Frei, AUNSPECIFIEDUNSPECIFIED
Neukomm, LJUNSPECIFIEDUNSPECIFIED
Kaufman, EUNSPECIFIEDUNSPECIFIED
Wollscheid, BUNSPECIFIEDUNSPECIFIED
Simard, MJUNSPECIFIEDUNSPECIFIED
Miska, EAUNSPECIFIEDUNSPECIFIED
Aebersold, RUNSPECIFIEDUNSPECIFIED
Gerber, APUNSPECIFIEDUNSPECIFIED
Hengartner, MOUNSPECIFIEDUNSPECIFIED
Date : 19 April 2012
Identification Number : https://doi.org/10.1101/gr.133330.111
Depositing User : Symplectic Elements
Date Deposited : 28 Mar 2017 14:42
Last Modified : 28 Mar 2017 14:42
URI: http://epubs.surrey.ac.uk/id/eprint/531404

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